X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fmsaclient.html;h=a20384902bc6bc8e245a462cf61e8d118db06a62;hb=79da59855c8eb16c5afef75d9d5701b7a39fb4c4;hp=889e1f5ab95e0a3c146f40e5463566c4208e3f66;hpb=4e9e138ca0eca9f7d3ec77742a6ca21c5ad80d9f;p=jalview.git
diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html
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@@ -21,34 +21,38 @@
Multiple Sequence Alignment Web Services
-
-Multiple sequence alignment services are accessed from the Web
-Service→Alignment menu. When an entry from this menu is
-selected, either the currently selected residues, or the whole
-sequence set (if there is no selection or only one sequence is
-selected) will be submitted for multiple sequence alignment.
-
+Multiple sequence alignment services can be accessed from either
+the Alignment or the JABAWS Alignment
+submenu of the Alignment Window's Web Service menu.
+When an entry from one of these menus is selected, either the currently
+selected residues, or the whole sequence set (if there is no selection
+or only one sequence is selected) will be submitted for multiple
+sequence alignment.
There are two kinds of multiple sequence alignment operations
-available:
-- alignment - where a new alignment is constructed from the input
-
-- realignment -
-where any aligned sequences will be used by the service
-to construct a profile based alignment of the remaining unaligned sequences.
-
+available:
+
+ - alignment - where a new alignment is constructed from
+ the input
+ - realignment - where any aligned sequences will be
+ used by the service to construct a profile based alignment of the
+ remaining unaligned sequences.
-
+The JABAWS Alignment services also offer a
+range of predefined alignment settings and the opportunity for you to
+define your own set of parameters for running the alingment program.
+Multiple Alignments of Sequences with hidden
+columns
+Multiple alignment services are 'column separable' analysis operations.
+If the input contains hidden
+columns then each visible segment of the input sequence set will be
+submitted for alignment separately, and the results concatenated (with
+the hidden regions preserved) once all alignment functions have
+completed. Each sub-job's state is reported in its own tab:
-Multiple Alignments of Sequences with hidden columns
-Multiple alignment services are 'column separable' analysis
-operations. If the input contains hidden columns then each
-visible segment of the input sequence set will be submitted for
-alignment separately, and the results concatenated (with the hidden
-regions preserved) once all alignment functions have completed. Each
-sub-job's state is reported in its own tab:
-
Multiple Multiple Sequence Alignment sub jobs running at
-once
+Multiple Multiple Sequence Alignment
+sub jobs running at once
+
+
